What is Quarto?

What is Quarto?

What is Quarto?

Why Quarto?

Literate programming

• Compilable code embedded in narrative text
• Text can be documentation or traditional report
• Widely used in scientific computing esp. in data science
• Facilitates open, reproducible research

What do you need to get started?

1. Quarto (download here)
2. Authoring tool (RStudio, Jupyter Lab, VS Code, any text editor)

• Quarto comes with RStudio
• R package quarto provides some extra functionality

YAML header

---
title: "Data Science for Industry assignment 1"
author: "Your name here"
format: html
editor: visual
execute:
  echo: true
---

• Demarcated by three dashes (---) on either end
• Note indentation
• The basic syntax of YAML uses key-value pairs in the format key: value
• https://quarto.org/docs/reference/formats/html.html

YAML header

---
title: "Introduction to Quarto"
date: "`r format(Sys.time(), '%d %B, %Y')`"
format: 
  revealjs:
      chalkboard: true
      scrollable: true
      theme: default
      footer: "STA5073Z Data Science for Industry"
      slide-number: true
      show-slide-number: print
      echo: true
---

Markdown text

• Plain text formatted using markdown syntax

Italics with *asterisks* or _underscores_.
Bold, with **asterisks** or __underscores__.
Combined emphasis with **asterisks and _underscores_**.
Strikethrough uses two tildes. ~~Scratch this.~~

• Italics with asterisks or underscores.
• Bold, with asterisks or underscores.
• Combined emphasis with asterisks and underscores.
• Strikethrough uses two tildes. Scratch this.

Markdown text

* Unordered list can use asterisks
- Or minuses
+ Or pluses

• Unordered list can use asterisks
• Or minuses
• Or pluses

Markdown text

* Unordered list can use asterisks, minuses or pluses
  - But indentation matters
    + But indentation matters
  + Indentation matters

• Unordered list can use asterisks, minuses or pluses
  • But indentation matters
    • But indentation matters
  • Indentation matters

Code

R Code:

```{r, echo = FALSE}
data(mtcars)
summary(mtcars$mpg)
```

Produces:

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  10.40   15.43   19.20   20.09   22.80   33.90 

Code

Chunk options as YAML with #|

```{r}
#| echo: false
data(mtcars)
summary(mtcars$mpg)
```

Produces:

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  10.40   15.43   19.20   20.09   22.80   33.90 

Code

R Code:

```{r, echo = FALSE}
data(mtcars)
summary(mtcars$mpg)
```

Syntax:

• 3 ticks on either side followed by {} with some code
• Ticks indicate start and end of code section
• {r, options} is knitr syntax saying how R should read and display code

Inserting figures

![A caption](images/Seec.png)

A caption

Subfigures

Stacking figures

::: {.r-stack}
![](images/gitproj1.png){.fragment width="600"}

![](images/gitproj2.png){.fragment width="550"}

![](images/gitproj3.png){.fragment width="500"}
:::

Tables

Markdown Syntax

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|   12  |  12  |    12   |    12  |
|  123  |  123 |   123   |   123  |
|    1  |    1 |     1   |     1  |

Output

Diagrams

• Quarto supports creating diagrams with Mermaid and Graphviz diagrams
• flowcharts, sequence diagrams, state diagrams, Gantt charts, and more
• Plain markdown-like text syntax

```{mermaid}
%%| echo: off
flowchart LR
  A[Hard edge] --> B(Round edge)
  B --> C{Decision}
  C --> D[Result one]
  C --> E[Result two]
```

Diagrams

• Quarto supports creating diagrams with Mermaid and Graphviz diagrams
• flowcharts, sequence diagrams, state diagrams, Gantt charts, and more
• Plain markdown-like text syntax

flowchart LR
  A[Hard edge] --> B(Round edge)
  B --> C{Decision}
  C --> D[Result one]
  C --> E[Result two]

Math notation

This generates an equation like $X\sim N(\mu,\sigma^2)$ that appears inline

This generates an equation like \(E = mc^{2}\) that appears inline

Put more important equations like $$X\sim N(\mu,\sigma^2)$$ onto their own line

Put more important equations like \[E = mc^{2}\] onto their own line

Callout blocks

:::{.callout-tip}
There are five types of callouts, including: 
`note`, `tip`, `warning`, `caution`, and `important`.
:::

• Callouts draw extra attention to certain concepts
• Type changes colour and icon of the callout
• Learn more on callouts here

Overview

Quarto supports a variety of formats for creating presentations, including:

• revealjs (HTML)
• PowerPoint
• Beamer (LaTeX/PDF)

These use the same markdown syntax as other documents, just adapt YAML and use #, ## to delineate slides.

HTML slides

---
title: "Quarto presentations"
author: "Me"
format: 
  revealjs:
      theme: default
---

## This is a slide

- Point 1
- Point 2

## Another slide

- More points
- More points

HTML slides

Powerpoint slides

---
title: "Quarto presentations"
author: "Me"
format: pptx
---

## This is a slide

- Point 1
- Point 2

## Another slide

- More points
- More points

Powerpoint slides

Powerpoint slides

---
title: "Quarto presentations"
author: "Me"
format:
  pptx:
    reference-doc: mytemplate.pptx
---

## This is a slide

- Point 1
- Point 2

## Another slide

- More points
- More points

Powerpoint slides

Overview

• Quarto Websites are just HTML files
• They share navigational elements and a common structure
• Mainly implemented through the YAML

YAML

---
project:
  type: website

website:
  title: "A Quarto Website"
  navbar:
    left:
      - href: index.qmd
        text: Home
      - addition.qmd
      - multiplication.qmd

format:
  html:
    theme: cosmo
    css: styles.css
    toc: true
---

index.qmd

---
title: "Welcome!"
---

This is a Quarto website.

To learn more about Quarto websites visit <https://quarto.org/docs/websites>.

addition.qmd

---
title: "Adding numbers in R"
---

To add numbers in R use `+`

```{r}
1 + 1
```

multiplication.qmd

---
title: "Multiplying numbers in R"
---

To multiply numbers in R use `*`

```{r}
2 * 3
```

Final website

Sources and further resources

• https://quarto.org/
• https://quarto.org/docs/guide/ (most of this lecture taken from here)
• https://quarto.org/docs/gallery/
• https://quarto.org/docs/reference/
• https://www.apreshill.com/blog/2022-04-we-dont-talk-about-quarto/